chore!: rename transform class and data dir to transformers

close #393

docs/source/reference/api/metakb.transform.civic.rst → docs/source/reference/api/metakb.transformers.base.rst

@@ -1,8 +1,8 @@
-metakb.transform.civic
-======================
+metakb.transformers.base
+========================
 
-.. automodule:: metakb.transform.civic
+.. automodule:: metakb.transformers.base
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config, model_computed_fields
+   :exclude-members: model_fields, model_config, model_computed_fields

docs/source/reference/api/metakb.transform.moa.rst → docs/source/reference/api/metakb.transformers.civic.rst

@@ -1,8 +1,8 @@
-metakb.transform.moa
-====================
+metakb.transformers.civic
+=========================
 
-.. automodule:: metakb.transform.moa
+.. automodule:: metakb.transformers.civic
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config, model_computed_fields
+   :exclude-members: model_fields, model_config, model_computed_fields

docs/source/reference/api/metakb.transform.base.rst → docs/source/reference/api/metakb.transformers.moa.rst

@@ -1,8 +1,8 @@
-metakb.transform.base
-=====================
+metakb.transformers.moa
+=======================
 
-.. automodule:: metakb.transform.base
+.. automodule:: metakb.transformers.moa
    :members:
    :undoc-members:
    :special-members: __init__
-   :exclude-members: model_fields, model_config, model_computed_fields
+   :exclude-members: model_fields, model_config, model_computed_fields

docs/source/reference/index.rst

@@ -60,6 +60,6 @@ Transformers
    :toctree: api/
    :template: module_summary.rst
 
-   metakb.transform.base
-   metakb.transform.civic
-   metakb.transform.moa
+   metakb.transformers.base
+   metakb.transformers.civic
+   metakb.transformers.moa

src/metakb/cli.py

@@ -34,7 +34,7 @@
 )
 from metakb.normalizers import check_normalizers as check_normalizer_health
 from metakb.schemas.app import SourceName
-from metakb.transform import CivicTransform, MoaTransform
+from metakb.transformers import CivicTransformer, MoaTransformer
 
 _logger = logging.getLogger(__name__)
 
@@ -451,12 +451,12 @@ def load_cdm(
 
         for src in sorted([s.value for s in SourceName]):
             pattern = f"{src}_cdm_{version}.json"
-            globbed = (APP_ROOT / "data" / src / "transform").glob(pattern)
+            globbed = (APP_ROOT / "data" / src / "transformers").glob(pattern)
 
             try:
                 path = sorted(globbed)[-1]
             except IndexError as e:
-                msg = f"No valid transform file found matching pattern: {pattern}"
+                msg = f"No valid transformation file found matching pattern: {pattern}"
                 raise FileNotFoundError(msg) from e
 
             load_from_json(path, driver)
@@ -534,12 +534,12 @@ async def update(
         sources = tuple(SourceName)
     for src in sorted([s.value for s in sources]):
         pattern = f"{src}_cdm_*.json"
-        globbed = (APP_ROOT / "data" / src / "transform").glob(pattern)
+        globbed = (APP_ROOT / "data" / src / "transformers").glob(pattern)
 
         try:
             path = sorted(globbed)[-1]
         except IndexError as e:
-            msg = f"No valid transform file found matching pattern: {pattern}"
+            msg = f"No valid transformation files found matching pattern: {pattern}"
             raise FileNotFoundError(msg) from e
 
         load_from_json(path, driver)
@@ -621,19 +621,21 @@ async def _transform_source(
     :param output_directory: custom directory to store output to -- use source defaults
         if not given
     """
-    transform_sources = {
-        SourceName.CIVIC: CivicTransform,
-        SourceName.MOA: MoaTransform,
+    transformer_sources = {
+        SourceName.CIVIC: CivicTransformer,
+        SourceName.MOA: MoaTransformer,
     }
     _echo_info(f"Transforming {source.as_print_case()}...")
     start = timer()
-    transformer: CivicTransform | MoaTransform = transform_sources[source](
+    transformer: CivicTransformer | MoaTransformer = transformer_sources[source](
         normalizers=normalizer_handler, harvester_path=harvest_file
     )
     harvested_data = transformer.extract_harvested_data()
     await transformer.transform(harvested_data)
     end = timer()
-    _echo_info(f"{source.as_print_case()} transform finished in {(end - start):.2f} s.")
+    _echo_info(
+        f"{source.as_print_case()} transformation finished in {(end - start):.2f} s."
+    )
     output_file = (
         output_directory / f"{source.value}_cdm_{_current_date_string()}.json"
         if output_directory
@@ -715,7 +717,7 @@ def _retrieve_s3_cdms() -> str:
         with tmp_path.open("wb") as f:
             file.Object().download_fileobj(f)
 
-        cdm_dir = APP_ROOT / "data" / source / "transform"
+        cdm_dir = APP_ROOT / "data" / source / "transformers"
         cdm_zip = ZipFile(tmp_path, "r")
         cdm_zip.extract(f"{source}_cdm_{newest_version}.json", cdm_dir)
 

src/metakb/transform/README.md → src/metakb/transformers/README.md

@@ -1,9 +1,9 @@
 # Transformations
-We take the harvested JSON from each source and transform this to our common data model. 
+We take the harvested JSON from each source and transform this to our common data model.
 
 
 ### Using the transformation modules
-The VICC normalizers must first be installed. 
+The VICC normalizers must first be installed.
 
 ```
 pip install thera-py
@@ -34,4 +34,4 @@ python3 -m gene.cli --normalizer="hgnc"
 [disease-normalizer](https://github.com/cancervariants/disease-normalization)
 ```
 python3 -m disease.cli --update_all --update_merged
-```
+```

src/metakb/transformers/__init__.py

@@ -0,0 +1,4 @@
+"""Transformations for sources."""
+
+from .civic import CivicTransformer  # noqa: F401
+from .moa import MoaTransformer  # noqa: F401

src/metakb/transform/base.py → src/metakb/transformers/base.py

@@ -1,4 +1,4 @@
-"""A module for the Transform base class."""
+"""A module for the Transformer base class."""
 
 import datetime
 import json
@@ -111,7 +111,7 @@ class TransformedData(BaseModel):
     documents: list[Document] = []
 
 
-class Transform(ABC):
+class Transformer(ABC):
     """A base class for transforming harvester data."""
 
     _methods: ClassVar[list[Method]] = [
@@ -234,13 +234,13 @@ def __init__(
         harvester_path: Path | None = None,
         normalizers: ViccNormalizers | None = None,
     ) -> None:
-        """Initialize Transform base class.
+        """Initialize Transformer base class.
 
         :param Path data_dir: Path to source data directory
         :param Optional[Path] harvester_path: Path to previously harvested data
         :param ViccNormalizers normalizers: normalizer collection instance
         """
-        self.name = self.__class__.__name__.lower().split("transform")[0]
+        self.name = self.__class__.__name__.lower().split("transformer")[0]
         self.data_dir = data_dir / self.name
         self.harvester_path = harvester_path
 
@@ -362,7 +362,7 @@ def _get_combination_therapy(
             Combination Therapy
         """
         components = []
-        source_name = type(self).__name__.lower().replace("transform", "")
+        source_name = type(self).__name__.lower().replace("transformers", "")
 
         for therapy in therapies:
             if source_name == SourceName.MOA:
@@ -516,15 +516,15 @@ def create_json(self, cdm_filepath: Path | None = None) -> None:
 
         :param cdm_filepath: Path to the JSON file where the CDM data will be
             stored. If not provided, will use the default path of
-            ``<APP_ROOT>/data/<src_name>/transform/<src_name>_cdm_YYYYMMDD.json``
+            ``<APP_ROOT>/data/<src_name>/transformers/<src_name>_cdm_YYYYMMDD.json``
         """
         if not cdm_filepath:
-            transform_dir = self.data_dir / "transform"
-            transform_dir.mkdir(exist_ok=True, parents=True)
+            transformers_dir = self.data_dir / "transformers"
+            transformers_dir.mkdir(exist_ok=True, parents=True)
             today = datetime.datetime.strftime(
                 datetime.datetime.now(tz=datetime.timezone.utc), DATE_FMT
             )
-            cdm_filepath = transform_dir / f"{self.name}_cdm_{today}.json"
+            cdm_filepath = transformers_dir / f"{self.name}_cdm_{today}.json"
 
         with cdm_filepath.open("w+") as f:
             json.dump(self.processed_data.model_dump(exclude_none=True), f, indent=2)

src/metakb/transform/civic.py → src/metakb/transformers/civic.py

@@ -26,11 +26,11 @@
     VariantTherapeuticResponseStudyPredicate,
     _VariantOncogenicityStudyQualifier,
 )
-from metakb.transform.base import (
+from metakb.transformers.base import (
     CivicEvidenceLevel,
     MethodId,
     TherapeuticProcedureType,
-    Transform,
+    Transformer,
 )
 
 _logger = logging.getLogger(__name__)
@@ -99,7 +99,7 @@ class SourcePrefix(str, Enum):
     ASH = "ASH"
 
 
-class CivicTransform(Transform):
+class CivicTransformer(Transformer):
     """A class for transforming CIViC to the common data model."""
 
     def __init__(
@@ -108,7 +108,7 @@ def __init__(
         harvester_path: Path | None = None,
         normalizers: ViccNormalizers | None = None,
     ) -> None:
-        """Initialize CIViC Transform class.
+        """Initialize CIViC Transformer class.
 
         :param data_dir: Path to source data directory
         :param harvester_path: Path to previously harvested CIViC data

src/metakb/transform/moa.py → src/metakb/transformers/moa.py

@@ -25,17 +25,17 @@
     VariantTherapeuticResponseStudyPredicate,
     _VariantOncogenicityStudyQualifier,
 )
-from metakb.transform.base import (
+from metakb.transformers.base import (
     MethodId,
     MoaEvidenceLevel,
     TherapeuticProcedureType,
-    Transform,
+    Transformer,
 )
 
 logger = logging.getLogger(__name__)
 
 
-class MoaTransform(Transform):
+class MoaTransformer(Transformer):
     """A class for transforming MOA resources to common data model."""
 
     def __init__(
@@ -44,7 +44,7 @@ def __init__(
         harvester_path: Path | None = None,
         normalizers: ViccNormalizers | None = None,
     ) -> None:
-        """Initialize MOAlmanac Transform class.
+        """Initialize MOAlmanac Transformer class.
 
         :param data_dir: Path to source data directory
         :param harvester_path: Path to previously harvested MOA data

tests/conftest.py

@@ -13,7 +13,7 @@
 
 TEST_DATA_DIR = Path(__file__).resolve().parents[0] / "data"
 TEST_HARVESTERS_DIR = TEST_DATA_DIR / "harvesters"
-TEST_TRANSFORM_DIR = TEST_DATA_DIR / "transform"
+TEST_TRANSFORMERS_DIR = TEST_DATA_DIR / "transformers"
 
 
 def pytest_addoption(parser):

tests/data/transform/diagnostic/civic_harvester.json → tests/data/transformers/diagnostic/civic_harvester.json

@@ -433,4 +433,4 @@
             ]
         }
     ]
-}
+}

tests/data/transform/prognostic/civic_harvester.json → tests/data/transformers/prognostic/civic_harvester.json

@@ -257,4 +257,4 @@
             ]
         }
     ]
-}
+}

tests/unit/transform/test_civic_transform_diagnostic.py → tests/unit/transformers/test_civic_transformer_diagnostic.py

@@ -4,19 +4,19 @@
 
 import pytest
 import pytest_asyncio
-from tests.conftest import TEST_TRANSFORM_DIR
+from tests.conftest import TEST_TRANSFORMERS_DIR
 
-from metakb.transform.civic import CivicTransform
+from metakb.transformers.civic import CivicTransformer
 
-DATA_DIR = TEST_TRANSFORM_DIR / "diagnostic"
+DATA_DIR = TEST_TRANSFORMERS_DIR / "diagnostic"
 FILENAME = "civic_cdm.json"
 
 
 @pytest_asyncio.fixture(scope="module")
 async def data(normalizers):
-    """Create a CIViC Transform test fixture."""
+    """Create a CIViC Transformer test fixture."""
     harvester_path = DATA_DIR / "civic_harvester.json"
-    c = CivicTransform(
+    c = CivicTransformer(
         data_dir=DATA_DIR, harvester_path=harvester_path, normalizers=normalizers
     )
     await c.transform()

tests/unit/transform/test_civic_transform_prognostic.py → tests/unit/transformers/test_civic_transformer_prognostic.py

@@ -4,19 +4,19 @@
 
 import pytest
 import pytest_asyncio
-from tests.conftest import TEST_TRANSFORM_DIR
+from tests.conftest import TEST_TRANSFORMERS_DIR
 
-from metakb.transform.civic import CivicTransform
+from metakb.transformers.civic import CivicTransformer
 
-DATA_DIR = TEST_TRANSFORM_DIR / "prognostic"
+DATA_DIR = TEST_TRANSFORMERS_DIR / "prognostic"
 FILENAME = "civic_cdm.json"
 
 
 @pytest_asyncio.fixture(scope="module")
 async def data(normalizers):
-    """Create a CIViC Transform test fixture."""
+    """Create a CIViC Transformer test fixture."""
     harvester_path = DATA_DIR / "civic_harvester.json"
-    c = CivicTransform(
+    c = CivicTransformer(
         data_dir=DATA_DIR, harvester_path=harvester_path, normalizers=normalizers
     )
     await c.transform()
@@ -79,7 +79,7 @@ def test_civic_cdm(
     check_method,
     check_transformed_cdm,
 ):
-    """Test that civic transform works correctly."""
+    """Test that civic transformation works correctly."""
     check_transformed_cdm(
         data,
         statements,

tests/unit/transform/test_civic_transform_therapeutic.py → tests/unit/transformers/test_civic_transformer_therapeutic.py

@@ -4,19 +4,19 @@
 
 import pytest
 import pytest_asyncio
-from tests.conftest import TEST_TRANSFORM_DIR
+from tests.conftest import TEST_TRANSFORMERS_DIR
 
-from metakb.transform.civic import CivicTransform
+from metakb.transformers.civic import CivicTransformer
 
-DATA_DIR = TEST_TRANSFORM_DIR / "therapeutic"
+DATA_DIR = TEST_TRANSFORMERS_DIR / "therapeutic"
 FILENAME = "civic_cdm.json"
 
 
 @pytest_asyncio.fixture(scope="module")
 async def data(normalizers):
-    """Create a CIViC Transform test fixture."""
+    """Create a CIViC Transformer test fixture."""
     harvester_path = DATA_DIR / "civic_harvester.json"
-    c = CivicTransform(
+    c = CivicTransformer(
         data_dir=DATA_DIR, harvester_path=harvester_path, normalizers=normalizers
     )
     harvested_data = c.extract_harvested_data()
@@ -33,5 +33,5 @@ def studies(civic_eid2997_study, civic_eid816_study, civic_eid9851_study):
 
 
 def test_civic_cdm(data, studies, check_transformed_cdm):
-    """Test that civic transform works correctly."""
+    """Test that civic transformation works correctly."""
     check_transformed_cdm(data, studies, DATA_DIR / FILENAME)